CRISPR-associated Cas3-HD domain (IPR006483)

Short name: CRISPR-assoc_Cas3_HD

Domain relationships



The CRISPR-Cas system is a prokaryotic defense mechanism against foreign genetic elements. The key elements of this defense system are the Cas proteins and the CRISPR RNA.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes [PMID: 17442114]. CRISPRs appear to provide acquired resistance against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA).

The defense reaction is divided into three stages. In the adaptation stage, the invader DNA is cleaved, and a piece of it is selected to be integrated as a new spacer into the CRISPR locus, where it is stored as an identity tag for future attacks by this invader. During the second stage (the expression stage), the CRISPR RNA (pre-crRNA) is transcribed and subsequently processed into the mature crRNAs. In the third stage (the interference stage), Cas proteins, together with crRNAs, identify and degrade the invader [PMID: 17379808, PMID: 16545108, PMID: 21699496].

The CRISPR-Cas systems have been sorted into three major classes. In CRISPR-Cas types I and III, the mature crRNA is generally generated by a member of the Cas6 protein family. Whereas in system III the Cas6 protein acts alone, in some class I systems it is part of a complex of Cas proteins known as Cascade (CRISPR-associated complex for antiviral defense). The Cas6 protein is necessary for crRNA production whereas the additional Cas proteins that form the Cascade complex are needed for crRNA stability [PMID: 24459147].

This entry represents the HD domain, which is found in a number of Cas proteins that tend to be found near CRISPR repeats. These domains can be found either separately or as the N-terminal region of Cas3, the helicase-containing CRISPR-associated protein. CRISPR loci appear to be mobile elements with a wide host range. The Cas3-type HD domain has nuclease activity against ssDNA and ssRNA [PMID: 21343909, PMID: 22009198].

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.
PROSITE profiles